Zecora returned to Zebrica during the First Great War and worked as a medicine woman and priestess at refugee camps. She was a huge help in keeping Zebricans’ hopes up and provided much needed food and care to those who had the brunt of the onslaught.

Now I can’t decide whether or not she returns to Equestria. She may find she is needed more in her homeland, rebuilding lives of her compatriots. Or she may return with the Mane 6 in order to advise them (primarilyw Twilight) in their future endeavors. Either way.